Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109) (characterized)
to candidate WP_011385595.1 AMB_RS16310 electron transfer flavoprotein subunit beta/FixA family protein
Query= BRENDA::D2RIQ2 (263 letters) >NCBI__GCF_000009985.1:WP_011385595.1 Length = 249 Score = 103 bits (258), Expect = 3e-27 Identities = 83/260 (31%), Positives = 131/260 (50%), Gaps = 21/260 (8%) Query: 1 MNIVVCVKQVPD-TAEMKIDPVTNNLVRDGVTNIMNPYDQYALETALQLKDELGA-HVTV 58 M ++V +K+V D ++++ + + V MNP+D+ A+E A++LK+ A V V Sbjct: 1 MKVLVAIKRVIDYNVKIRVKSDGSGVETQNVKFSMNPFDEIAVEEAVRLKEAGKATEVVV 60 Query: 59 ITMGPPHAESVLRDCLAVGADEAKLVSDRAFGGADTLATSAAMANTIKHF---GVPDLIL 115 +++GP A LR LA+GAD LV D +A +K P LI+ Sbjct: 61 VSIGPAAASETLRTALAMGADRGVLVQ------TDDEVQPLGVAKVLKALVAKEAPGLII 114 Query: 116 CGRQAIDGDTAQVGPEIAEHLGLPQVTAALKVQVKDDTVVVDRDNEQMSMTFTMKMPCVV 175 G+QAID D+ Q G +A LG Q T A KV++ D + V R+ + T ++K+P VV Sbjct: 115 LGKQAIDDDSNQTGQMLAALLGCAQGTFASKVEIGADAITVTREVDGGLETVSLKLPAVV 174 Query: 176 TV-MRSKDLRFASIRGKMKARKAEIPVYTAAALEIPLDIIGKAGSPTQVMKSFTPKVTQV 234 T +R + R+AS+ MKA+K P+ T + ++ +D+ +P V S + Sbjct: 175 TTDLRLNEPRYASLPNIMKAKKK--PIDTVSPADLGVDV-----APRLVTLSVAEPPKRS 227 Query: 235 HGEIFDDEDPAVAVDKLVNK 254 G D A VDKL N+ Sbjct: 228 AG--IKVADVAALVDKLKNE 245 Lambda K H 0.318 0.133 0.375 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 137 Number of extensions: 7 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 263 Length of database: 249 Length adjustment: 24 Effective length of query: 239 Effective length of database: 225 Effective search space: 53775 Effective search space used: 53775 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory